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Feng T, Lai C, Yuan Q, Yang W, Yao Y, Du M, Zhong D, Wang S, Yang Q, Shang J, Shi Y, Huang X. Non-invasive assessment of liver fibrosis by serum metabolites in non-human primates and human patients. iScience 2023; 26:107538. [PMID: 37636059 PMCID: PMC10448158 DOI: 10.1016/j.isci.2023.107538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 03/30/2023] [Accepted: 07/28/2023] [Indexed: 08/29/2023] Open
Abstract
Liver fibrosis, a rising cause of chronic liver diseases, could eventually develop into cirrhosis and liver failure. Current diagnosis of liver fibrosis relies on pathological examination of hepatic tissues acquired from percutaneous biopsy, which may produce invasive injuries. Here, for non-invasive assessment of liver fibrosis, we applied comparative multi-omics in non-human primates (rhesus macaques) and subsequent serum biopsy in human patients. Global transcriptomics showed significant gene enrichment of metabolism process, in parallel with oxidative stress and immune responses in fibrotic primates. Targeted metabolomics were concordant with transcriptomic patterns, identifying elevated lipids and porphyrin metabolites during hepatic fibrosis. Importantly, liquid biopsy results validated that specific metabolites in the serum (e.g., biliverdin) were highly diagnostic to distinguish human patients from healthy controls. Findings describe the interconnected transcriptional and metabolic network in primate liver fibrosis and provide potential indices for non-invasive detection of liver fibrosis in humans.
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Affiliation(s)
- Tianhang Feng
- Department of Hepatobiliary and Pancreatic Surgery, Sichuan Academy of Medical Sciences, Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Chunyou Lai
- Department of Hepatobiliary and Pancreatic Surgery, Sichuan Academy of Medical Sciences, Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Qiuyun Yuan
- State Key Laboratory of Oral Diseases, National Center of Stomatology, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - Wanchun Yang
- Department of Neurosurgery, West China Hospital, Sichuan University, Chengdu, China
| | - Yutong Yao
- Department of Hepatobiliary and Pancreatic Surgery, Sichuan Academy of Medical Sciences, Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Mengze Du
- Department of Neurosurgery, West China Hospital, Sichuan University, Chengdu, China
| | - Deyuan Zhong
- Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Sijia Wang
- Department of Hepatobiliary and Pancreatic Surgery, Sichuan Academy of Medical Sciences, Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Qinyan Yang
- Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Jin Shang
- Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Ying Shi
- Department of Hepatobiliary and Pancreatic Surgery, Sichuan Academy of Medical Sciences, Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Xiaolun Huang
- Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
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Wang L, Zhang J, Peng D, Tian Y, Zhao D, Ni W, Long J, Li J, Zeng Y, Wu Z, Tang Y, Wang Z. High-Quality Genome Assembly of Olea europaea subsp. cuspidata Provides Insights Into Its Resistance to Fungal Diseases in the Summer Rain Belt in East Asia. FRONTIERS IN PLANT SCIENCE 2022; 13:879822. [PMID: 35656016 PMCID: PMC9152427 DOI: 10.3389/fpls.2022.879822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Accepted: 03/14/2022] [Indexed: 06/15/2023]
Abstract
The olive tree (Olea europaea L.) is the most iconic fruit crop of the Mediterranean Basin. Since the plant was introduced to China in the 1960s, the summer rain climate makes it susceptible to pathogens, leading to some olive diseases. Olea europaea L. subsp. cuspidata is natively distributed in the Yunnan province of China. It has a smaller fruit size, lower oil content, and higher resistance compared to subsp. europaea, which makes subsp. cuspidata a critical germplasm resource to be investigated. Here, a high-quality genome of subsp. cuspidata with 1.38 Gb in size was assembled and anchored onto 23 pseudochromosomes with a mounting rate of 85.57%. It represents 96.6% completeness [benchmarking universal single-copy orthologs (BUSCO)] with a contig N50 of 14.72 Mb and a scaffold N50 of 52.68 Mb, which shows a significant improvement compared with other olive genomes assembled. The evaluation of the genome assembly showed that 92.31% of resequencing reads and an average of 96.52% of assembled transcripts could be aligned to the assembled genome. We found that a positively selected gene, evm.model.Chr16.1133, was shared with the results of transcriptome analysis. This gene belongs to the susceptible gene and negatively regulates the disease resistance process. Furthermore, we identified the Cercospora genus which causes the leaf spot disease in the infected leaves. The high-quality chromosome-level genomic information presented here may facilitate the conservation and utilization of germplasm resources of this subspecies and provide an essential genetic basis for further research into the differences in oil content and resistance between subsp. cuspidata and europaea.
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Affiliation(s)
- Li Wang
- Key Laboratory of Silviculture of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Jianguo Zhang
- Key Laboratory of Silviculture of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Collaborative Innovation Center of Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Dan Peng
- Kunpeng Institute of Modern Agriculture at Foshan, Foshan, China
| | - Yang Tian
- Key Laboratory of Silviculture of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Dandan Zhao
- Key Laboratory of Silviculture of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Wanning Ni
- Key Laboratory of Silviculture of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Jinhua Long
- Key Laboratory of Silviculture of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Jinhua Li
- Key Laboratory of Silviculture of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Yanfei Zeng
- Key Laboratory of Silviculture of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Collaborative Innovation Center of Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Zhiqiang Wu
- Kunpeng Institute of Modern Agriculture at Foshan, Foshan, China
| | - Yiyun Tang
- Ecological Restoration and Industrial Development Workstation, Nujiang State Forestry and Grassland Bureau of Yunnan Province, Kunming, China
| | - Zhaoshan Wang
- Key Laboratory of Silviculture of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Collaborative Innovation Center of Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
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